In [1]:
"""
Created on Sat Mar 30 07:59:28 2024

@author: marik
""";
In [2]:
import sys
sys.path.append('..')
import pandas as pd
import tomotree as tomo
import matplotlib.pyplot as plt
import numpy as np

Read the data¶

In [3]:
# csv_tof = 'tomoWood_data/3_TOFDefEcc.txt'
# csv_nodes = 'tomoWood_data/3_posRecDefEcc.txt'
csv_tof = 'tomoWood_data/1_TOFHealthy.txt'
csv_nodes = 'tomoWood_data/1_posRecHealthy.txt'
image_name = "tomoWood_data/1_PhotoHealthy.png"
scale = 2.8
shift = np.array([350,300])
df = pd.read_csv(csv_nodes, sep='\t',header=None)
df = df.values*1000
nodes = df.copy()
nodes = nodes - nodes.mean(axis=0)

n2 = nodes.copy() # for aligning to image
n2[:,1] = -n2[:,1]
n2 = n2*scale + shift
im = plt.imread(image_name)
plt.imshow(im,zorder=1)
plt.scatter(*n2.T, s=np.arange(1,17)*5)
plt.title("Node positions. The size of the node corresponds to the node number.")
plt.gca().set_aspect(1);
No description has been provided for this image
In [4]:
df = pd.read_csv(csv_tof, sep='\t',header=None)
df.columns.name = "source node number"
df.columns = range(1,len(df.columns)+1)
df.index = range(1,len(df.index)+1)
plt.imshow(df.values.astype(float), cmap='Greys',
       origin='lower')
plt.gca().set_aspect(0.5)
d = tomo.roll_table(df.values)*1000
No description has been provided for this image
In [5]:
df.plot(subplots=[np.arange(1,9),np.arange(9,17)])
# plt.plot(*nodes.T,'o')
Out[5]:
array([<Axes: >, <Axes: >], dtype=object)
No description has been provided for this image
In [6]:
t=tomo.Tomo(nodes=nodes, times=d.values, nx=31, ny=31)
t.plot(speed_min=1400, speed_max=1600, rays=False)
plt.suptitle("Speed as a mean value of ray speeds")
Out[6]:
Text(0.5, 0.98, 'Speed as a mean value of ray speeds')
No description has been provided for this image
In [7]:
speeds = t.speeds
speeds.style.highlight_max().format(precision=0).highlight_min(color='red')
Out[7]:
Source node 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
Receiver node                                
1 nan 1450 1456 1735 1487 1673 1562 1549 1473 1384 1509 1427 1628 1463 1304 2549
2 3150 nan 1369 1400 1462 1517 1387 1521 1537 1431 1491 1436 1545 1562 1434 1569
3 1428 1706 nan 1203 1412 1486 1601 1409 1503 1535 1421 1436 1598 1614 1508 1449
4 1530 1800 1390 nan 1263 1312 1317 1380 1573 1564 1569 1390 1566 1716 1671 1654
5 1353 1411 1791 1405 nan 1345 1153 2177 1673 1611 1449 1526 1592 1830 1720 1644
6 1460 1502 1477 1471 1140 nan 1515 1360 1589 1619 1629 1539 1530 1697 1720 1686
7 1336 1347 1390 1444 1320 1138 nan 3686 2154 1775 1599 1533 1572 1589 1671 1686
8 1553 1338 1337 1579 1590 1324 1401 nan 2228 1844 1618 1642 1463 1579 1482 1677
9 1473 1435 1402 1635 1545 1681 1539 1919 nan 1256 1723 1436 1284 1489 1529 1498
10 1432 1431 1352 1505 1673 1620 1753 1424 3522 nan 1452 1403 1391 1547 1649 1613
11 1583 1455 1421 1482 1636 1840 1614 1541 1259 1994 nan 1411 1330 1540 1535 1707
12 1676 1487 1441 1390 1605 1717 1737 1570 1565 1462 1400 nan 1466 1585 1387 1737
13 1503 1620 1477 1580 1592 1563 1694 1525 1411 1396 1983 1323 nan 1324 1430 1613
14 1497 1563 1491 1541 1559 1697 1571 1563 1517 1562 2409 1810 1504 nan 2459 1821
15 1761 1700 1522 1578 1648 1591 1671 1520 1464 1432 1768 1528 1742 1463 nan 3262
16 1687 1551 1669 1582 1564 1551 1760 1677 1486 1477 1704 1517 1774 1396 1277 nan
In [8]:
diff = (speeds - speeds.T)/2
diff.style.highlight_max().format(precision=0).highlight_min(color='red')
Out[8]:
Source node 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
Receiver node                                
1 nan -850 14 102 67 106 113 -2 0 -24 -37 -124 63 -17 -229 431
2 850 nan -169 -200 25 7 20 92 51 0 18 -26 -38 -1 -133 9
3 -14 169 nan -93 -189 4 105 36 50 92 0 -3 60 61 -7 -110
4 -102 200 93 nan -71 -80 -64 -100 -31 29 44 0 -7 87 47 36
5 -67 -25 189 71 nan 102 -83 294 64 -31 -93 -39 0 135 36 40
6 -106 -7 -4 80 -102 nan 188 18 -46 -1 -105 -89 -17 0 65 67
7 -113 -20 -105 64 83 -188 nan 1142 307 11 -8 -102 -61 9 0 -37
8 2 -92 -36 100 -294 -18 -1142 nan 154 210 39 36 -31 8 -19 0
9 0 -51 -50 31 -64 46 -307 -154 nan -1133 232 -65 -64 -14 33 6
10 24 0 -92 -29 31 1 -11 -210 1133 nan -271 -29 -3 -7 109 68
11 37 -18 0 -44 93 105 8 -39 -232 271 nan 6 -326 -434 -116 1
12 124 26 3 0 39 89 102 -36 65 29 -6 nan 71 -112 -70 110
13 -63 38 -60 7 0 17 61 31 64 3 326 -71 nan -90 -156 -80
14 17 1 -61 -87 -135 0 -9 -8 14 7 434 112 90 nan 498 213
15 229 133 7 -47 -36 -65 0 19 -33 -109 116 70 156 -498 nan 992
16 -431 -9 110 -36 -40 -67 37 0 -6 -68 -1 -110 80 -213 -992 nan
In [9]:
t.check_triangle_inequality()
Out[9]:
'Triangle inequality failed 98 out of 3360 which is 3%.'
In [10]:
ax = t.plot_angular_dependence()
ax.set(ylim=(None,2000))
Out[10]:
[(1010.6944579547201, 2000.0)]
No description has been provided for this image

EBSI method¶

In [11]:
t1=tomo.Tomo(nodes=nodes, times=d.values,nx=61,ny=61)
t1.do_EBSI_method()
Out[11]:
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        <tomotree.Cell object at 0x729829ebbc20>,
        <tomotree.Cell object at 0x729829ebbc50>,
        <tomotree.Cell object at 0x729829ebbc80>,
        <tomotree.Cell object at 0x729829ebbcb0>,
        <tomotree.Cell object at 0x729829ebbce0>,
        <tomotree.Cell object at 0x729829ebbd10>,
        <tomotree.Cell object at 0x729829ebbd40>,
        <tomotree.Cell object at 0x729829ebbd70>,
        <tomotree.Cell object at 0x729829edc740>,
        <tomotree.Cell object at 0x729829edc770>,
        <tomotree.Cell object at 0x729829edc7a0>,
        <tomotree.Cell object at 0x729829edc7d0>,
        <tomotree.Cell object at 0x729829edc800>,
        <tomotree.Cell object at 0x729829edc830>,
        <tomotree.Cell object at 0x729829edc860>,
        <tomotree.Cell object at 0x729829edc890>,
        <tomotree.Cell object at 0x729829edc8c0>,
        <tomotree.Cell object at 0x729829edc8f0>,
        <tomotree.Cell object at 0x729829edd2b0>,
        <tomotree.Cell object at 0x729829edd2e0>,
        <tomotree.Cell object at 0x729829edd310>,
        <tomotree.Cell object at 0x729829edd340>,
        <tomotree.Cell object at 0x729829edd370>,
        <tomotree.Cell object at 0x729829edd3a0>,
        <tomotree.Cell object at 0x729829edd3d0>,
        <tomotree.Cell object at 0x729829edd400>,
        <tomotree.Cell object at 0x729829edd430>,
        <tomotree.Cell object at 0x729829edd460>,
        <tomotree.Cell object at 0x72982a0286b0>,
        <tomotree.Cell object at 0x72982a028560>,
        <tomotree.Cell object at 0x72982a028590>,
        <tomotree.Cell object at 0x72982a0285c0>,
        <tomotree.Cell object at 0x72982a028470>,
        <tomotree.Cell object at 0x72982a0284a0>,
        <tomotree.Cell object at 0x72982a0284d0>,
        <tomotree.Cell object at 0x72982a15d730>,
        <tomotree.Cell object at 0x72982a15d760>,
        <tomotree.Cell object at 0x72982a15d790>,
        <tomotree.Cell object at 0x729829ede6c0>,
        <tomotree.Cell object at 0x729829ede6f0>,
        <tomotree.Cell object at 0x729829ede720>,
        <tomotree.Cell object at 0x729829ede750>,
        <tomotree.Cell object at 0x729829ede780>,
        <tomotree.Cell object at 0x729829ede7b0>,
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        <tomotree.Cell object at 0x729829ede810>,
        <tomotree.Cell object at 0x729829ede840>,
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        <tomotree.Cell object at 0x729829edf290>,
        <tomotree.Cell object at 0x729829edf2c0>,
        <tomotree.Cell object at 0x729829edf2f0>,
        <tomotree.Cell object at 0x729829edf320>,
        <tomotree.Cell object at 0x729829edf350>,
        <tomotree.Cell object at 0x729829edf380>,
        <tomotree.Cell object at 0x729829edfda0>,
        <tomotree.Cell object at 0x729829edfdd0>,
        <tomotree.Cell object at 0x729829edfe00>,
        <tomotree.Cell object at 0x729829edfe30>,
        <tomotree.Cell object at 0x729829edfe60>,
        <tomotree.Cell object at 0x729829edfe90>,
        <tomotree.Cell object at 0x729829edfec0>], dtype=object)}
In [12]:
limits = t1.limit_cell_plot_velocities(4)
t1.plot(rays=False, **limits)
Out[12]:
<Axes: >
No description has been provided for this image

SIRT method¶

In [13]:
t2=tomo.Tomo(nodes=nodes, times=d.values, nx=31, ny=31)
t2.do_SIRT_method(speed_min=800, speed_max=1800)
Out[13]:
'SIRT finished in 513 ms.\nSpeed interval: min=800.0 for 10 segments, max=1800.0  for 2016 segments'
In [14]:
t2.plot(speed_min=800, speed_max=1800)
plt.suptitle("SIRT method")
Out[14]:
Text(0.5, 0.98, 'SIRT method')
No description has been provided for this image

ERSM method with tangential velocities fixed¶

In [15]:
t3=tomo.Tomo(nodes=nodes, times=d.values, nx=51, ny=51, symmetric=True)
t3.do_ERSM_method()
In [16]:
limits = t3.limit_cell_plot_velocities(4)
t3.plot(grid=True, rays=False, **limits)
plt.suptitle("ERSM method with fixed tangential velocity")
Out[16]:
Text(0.5, 0.98, 'ERSM method with fixed tangential velocity')
No description has been provided for this image

ERSM method¶

Do not fix nonradial velocity

In [17]:
t4=tomo.Tomo(nodes=nodes, times=d.values, nx=51, ny=51, symmetric=True)
t4.do_ERSM_method(fix_velocity_EBSI_function=lambda x, y: x )
In [18]:
t4.plot(speed_min=1400, speed_max=1600)
Out[18]:
<Axes: >
No description has been provided for this image
In [19]:
limits = t4.limit_cell_plot_velocities(4)
t4.plot(rays=False, **limits)
plt.suptitle("ERSM method, tangential velocity not fixed")
Out[19]:
Text(0.5, 0.98, 'ERSM method, tangential velocity not fixed')
No description has been provided for this image
In [ ]:
In [ ]: